Method for label-free multiple analyte sensing, biosensing and diagnostic assay

ABSTRACT

Methods and systems for label-free multiple analyte sensing, biosensing and diagnostic assay chips consisting of an array of photonic crystal microcavities along a single photonic crystal waveguide are disclosed. The invention comprises an on-chip integrated microarray device that enables detection and identification of multiple species to be performed simultaneously using optical techniques leading to a high throughput device for chemical sensing, biosensing and medical diagnostics. Other embodiments are described and claimed.

I. CROSS REFERENCE TO RELATED APPLICATIONS

The application is a continuation application of U.S. patent applicationSer. No. 13/607,793, titled “Photonic Crystal MicroArray Layouts forEnhanced Sensitivity and Specificity of Label-Free Multiple AnalyteSensing, Biosensing and Diagnostic Assay,” filed Sep. 9, 2012, which isa continuation-in-part application of U.S. patent application Ser. No.12/462,311, titled “Photonic Crystal Microarray Device for Label-FreeMultiple Analyte Sensing, Biosensing and Diagnostic Assay Chips”, filedAug. 3, 2009, now U.S. Pat. No. 8,293,177, issued Oct. 23, 2012, thecontents of which are all hereby Incorporated by reference.

II. BACKGROUND

Field of the Invention

This invention relates generally to the field of optical and medicaldevices, and more specifically to an apparatus and method for microarrayimplementation for the detection of multiple analytes such as chemicalagents and biological molecules using photonic crystals.

Background of the Invention

Label-free optical sensors based on photonic crystals have beendemonstrated as a highly sensitive potential method for performing alarge range of biochemical and cell-based assays. For backgroundinformation on photonic crystals, the reader is directed toJoannopoulos, J. D., R. D. Meade, and J. N. Winn, Photonic Crystals,1995 Princeton, N.J.: Princeton University Press. Tight confinement ofthe optical field in photonic crystal microcavities leads to a stronginteraction with the surrounding ambient in the vicinity of themicrocavity, thereby leading to large sensitivity to changes inrefractive index of the ambient. Much of the research in photoniccrystal devices has relied on enhancing refractive index sensitivity toa single analyte (Lee M. R., Fauchet M., “Nanoscale microcavity sensorfor single particle detection,” Optics Letters 32, 3284 (2007)).Research on photonic crystals for multiple analyte sensing has focusedon one-dimensional photonic crystal grating-like structures (see patentsUS20080225293 and US20030027328) that measure the resonant peakreflected wavelengths; such sensors have wide linewidths of the resonantpeaks due to one-dimensional confinement and do not utilize the fullpotential of narrow resonant linewidths of two-dimensional photoniccrystal microcavities. Furthermore, measurements are made from eachsensor element in the array in a serial process, requiring multiplesources and detectors for parallel sensing beyond a single element.Research has been performed with one-dimensional photonic crystalmicrocavities coupled to ridge waveguides (See Mandal S. and EricksonD., “Nanoscale optofluidic sensor arrays”, Optics Express 16, 1623(2008)). One dimensional photonic crystal microcavities, in addition topoor optical confinement, do not utilize the slow light effect due toreduced group velocity in two-dimensional photonic crystal waveguidesthat would otherwise enhance coupling efficiency and thereby improvesignal-to-noise ratio of sensing. Demonstrated two dimensional photoniccrystal waveguide biosensors rely on shifts of the stop-gap (seeSkivesen N. et al., “Photonic crystal waveguide biosensor”, OpticsExpress 15, 3169 (2007)) or shifts of the resonant peak of an isolatedmicrocavity (see Chakravarty S. et al., “Ion detection with photoniccrystal microcavities”, Optics Letters 30, 2578 (2005)). In either case,the design is not suitable for the fabrication of microarrays formultiple analyte sensing.

Two dimensional photonic crystal microcavities integrated withtwo-dimensional photonic crystal waveguides offer the possibility ofintegrating the high quality-factor resonances of two-dimensionalphotonic crystal microcavities with the slow light effect oftwo-dimensional photonic crystal waveguides for high sensitivity, highsignal-to-noise ratio sensing. Furthermore, multiple photonic crystalmicrocavities can be simultaneously arrayed along a single photoniccrystal waveguide, so that a single measurement can be performed inparallel to elicit the response from multiple sensor elements, therebyincreasing measurement throughput and reducing cost. An array of twosensors demonstrated using two-dimensional photonic crystalmicrocavities uses multiple ridge waveguides between individual photoniccrystal microcavities. Coupling between photonic crystal waveguides andridge waveguides introduces additional significant transmission loss ateach interface, thereby significantly reducing signal-to-noise ratio aseach microcavity is added for multiple sensing. The design demonstratedby Guillermain et al. (see Guillermain E., Fauchet P. M., “Multi-channelsensing with resonant microcavities coupled to a photonic crystalwaveguide,” JWA 45, CLEO Conference (2009)) in effect employs multiplephotonic crystal waveguides and also employs microcavities withsignificantly poor quality factors that make the designs unsuitable forhigh sensitivity sensing. Better designs are needed in the art torealize photonic crystal microarray devices that efficiently couplelight from ridge waveguides to a single photonic crystal waveguide,wherein multiple photonic crystal microcavities with high qualityfactors and covering a large bandwidth for sensing are coupled to asingle photonic crystal waveguide for high sensitivity multiple sensing.

A standard on-chip multiple protein patterning technique usinglithography typically requires a pre-bake resist temperature of 100° C.or higher. At the very least, temperatures this high compromise or alterbiological functionality, and at the very worst they may destroy itsfunction. Most proteins are stable in vivo at a temperature of 37° C.,but this stability is dependent on chaperone proteins that maintain theproper conformation of other proteins in cells. Since proteins in vitrolack these chaperone proteins, they must be maintained at even lowertemperatures to prevent denaturation and loss of function. Designs areneeded to enable patterning of different kinds of biomolecules inaqueous phase to preserve functionality of biomolecules.

Designs are needed in the art to integrate two-dimensional photoniccrystal microcavities with two-dimensional photonic crystal waveguidesfor multiple analyte sensing and designs are further needed to patternmultiple biomolecules, of different constitutions, on the photoniccrystal substrate while preserving their functionality.

III. SUMMARY

One embodiment of the invention provides a sensor comprising asemiconductor material core with high dielectric constant, supported onthe bottom by a low dielectric constant cladding. A triangular latticeof photonic crystal holes is etched into the substrate. The photoniccrystal waveguide is defined by filling a single row of holes, frominput ridge waveguide transition to output ridge waveguide transitionwith the semiconductor core material. A photonic crystal microcavity issimilarly defined by filing a few holes with semiconductor corematerial. Multiple photonic crystal microcavities are patterned at adistance of three lattice constants from the photonic crystal waveguide.The distance between individual photonic crystal microcavities is 10lattice periods. The high dielectric constant core with structuredphotonic crystal waveguide and photonic crystal microcavities, togetherwith the low dielectric constant cladding, form the photonic crystalmicroarray structure. Light is coupled into the photonic crystalwaveguide from a ridge waveguide. Light is out-coupled from the photoniccrystal waveguide to an output ridge waveguide. When a broadband lightsource is input to the photonic crystal waveguide, wavelengthscorresponding to the resonant wavelengths of the individualmicrocavities are coupled to the corresponding microcavities. As aresult, minima are observed in the transmission spectrum correspondingto the dropped wavelength of each photonic crystal microcavity.Depending upon the wavelength range of interrogation, the period of thesub-wavelength lattice can vary from 50 nm to 1500 nm and the depth ofthe lattice structure can vary from 0.4 to 0.7 times the latticeperiodicity above. The semiconductor material can be silicon (or anyGroup IV material), gallium arsenide (or any III-V semiconductor) or anysemiconductor material with high refractive index. The substrate can beany Group IV material corresponding to the Group IV core material, orany substrate suitable to grow the III-V core material. Above themicrocavity, a thin film of target binding molecules that areimmobilized on the microcavity surfaces, each microcavity surface beingcoated with an exclusive target molecule or biomolecule, forms thedielectric coating. The one or more binding molecules are free ofdetection labels. The one or more specific binding substances are thusarranged in an array on the microcavities, along the photonic crystalwaveguide. A single transmission spectrum therefore probes the bindingevents on multiple microcavities. A binding event on a specificmicrocavity shifts the corresponding transmission minimum and leads to asensing event for the specific microcavity. Analyzed biomolecules can beproteins, DNA, RNA, small molecules or genes. Arrays of microcavitiestherefore lead to a multiple analyte sensing device that increases themeasurement throughput of the device, in addition to the obvioussensitivity enhancements achieved by using a two-dimensional photoniccrystal waveguide coupled to two-dimensional photonic crystalmicrocavities.

To summarize:

The primary objective of the invention is to provide an integratedphotonic crystal microarray with compact size that can be monolithicallyintegrated with different kinds of biomolecules such as proteins,nucleic acids, DNA, RNA or small molecules to implement a personalizeddiagnostic chip.

The second objective of the invention is to eliminate the need forlabeling of biomolecule and biomolecule conjugates for on-chip detectionand thereby reduce microarray costs associated with biomoleculelabeling.

The third objective of the invention is to significantly increasemeasurement throughput from devices by signal collection and analysisfrom multiple elements of a microarray in a single measurement asopposed to individual element measurement in contemporary systems.

The fourth objective of the invention is to implement a novellithography scheme on a CMOS chip that avoids high temperature processesassociated with photolithography and chemical etching for the patterningof multiple biomolecules and thereby preserves biomolecule functionalityin aqueous phase at room temperatures or even colder if necessary.

Other objectives and advantages of the present invention will becomeapparent from the following descriptions, taken in connection with theaccompanying drawings, wherein, by way of illustration and example, anembodiment of the present invention is disclosed.

IV. BRIEF DESCRIPTION OF THE DRAWINGS

The drawings constitute a part of this specification and includeexemplary embodiments of the present invention, which may be embodied invarious forms. It is to be understood that in some instances variousaspects of the present invention may be shown exaggerated or enlarged tofacilitate an understanding of the invention.

A more complete and thorough understanding of the present invention andbenefits thereof may be acquired by referring to the followingdescription together with the accompanying drawings, in which likereference numbers indicate like features, and wherein:

FIG. 1A is a top view of one embodiment of a photonic crystal microarraydevice based on an array of N photonic crystal microcavities coupled toa photonic crystal waveguide. In FIG. 1A, N is chosen arbitrarily as 4for space constraints. FIG. 1B is an enlarged section of FIG. 1A.

FIG. 2 is a cross-sectional view of the device shown in FIG. 1B takenalong line A-A′.

FIG. 3 is a top view of one embodiment of a photonic crystal microarraydevice based on an array of N photonic crystal microcavities coupled toa photonic crystal waveguide where each photonic crystal microcavity iscoated with a different biomolecule.

FIG. 4 is a top view of the field intensity pattern of a guided mode ofa photonic crystal waveguide depicted in FIG. 1B taken along line A-A′.

FIG. 5 is a top view of the field intensity pattern of a photoniccrystal microcavity defect mode for the linear microcavity depicted inFIG. 1B taken along line B-B′.

FIG. 6 illustrates a typical diagram of the dispersion relation of aphotonic crystal waveguide and individual microcavities with resonantmodes in the low dispersion low group velocity region for enhanced modecoupling from waveguide to microcavity.

FIG. 7A shows a top view of a functional photonic crystal waveguide withtwo representatively coupled photonic crystal microcavities along thelength of the photonic crystal waveguide. Two (2) microcavities arechosen, as a representative number for n. n can vary from 1 to N (N→∞).FIG. 7B shows the transmission spectrum of the embodiment depicted inFIG. 7A.

FIG. 8A shows a top view of a functional photonic crystal microcavity.Elements that are geometrically tuned in size and/or position areindicated. FIG. 8B shows the transmission spectrum when tworepresentative photonic crystal microcavities of the embodiment depictedin FIG. 8A are coupled to the functional photonic crystal waveguide inFIG. 1A and FIG. 1B. FIG. 8C shows a top view of a functional photoniccrystal microcavity where more than just the adjacent void columnarmembers have been shifted. FIG. 8D shows a top view of a compositemicrocavity comprising two mirrored functional photonic crystalmicrocavities. FIG. 8E shows a top view of functional photonic crystalmicrocavities oriented along the +60 degrees orientation of the crystallattice. FIG. 8F shows a top view of functional photonic crystalmicrocavities oriented along the −60 degrees orientation of the crystallattice. It is shown that geometry tuning can shift resonant frequenciesand optimum spacing between microcavities ensures no cross-talk betweenadjacent microcavities.

FIG. 9 shows another transmission spectrum of a functional photoniccrystal waveguide with two representatively coupled photonic crystalmicrocavities of the embodiment depicted in FIG. 8A along the length ofthe functional photonic crystal waveguide in FIG. 1A and FIG. 1B. Two(2) microcavities are chosen, as a representative number for n. n canvary from 1 to N (N→∞). It is shown that geometry tuning can shiftresonant frequencies and thereby allows the potential to couple Nphotonic crystal microcavities in an array, each with a small differencein geometry, hence a small difference in resonant frequency and hencepotential of the device to respond to multiple analytes, molecules andbiomolecules.

FIG. 10A through FIG. 10I show the steps in the fabrication ofmicrofluidic channels on patterned silicon chips for biomoleculedelivery and subsequent removal to create arrays of biomolecule coatedphotonic crystal microcavities.

FIG. 11 is a top view of the device in FIG. 10G and FIG. 10H.

FIG. 12A and FIG. 12B show the changes in the transmission spectrum whena sandwiched measurement is performed that involves introduction of asecondary molecule or biomolecule after the introduction of the analytemolecule or biomolecule, resulting in amplification of the sensitivitydetection and enhancement of the specificity detection.

V. DETAILED DESCRIPTION Detailed Description of the Invention

In accordance with a preferred embodiment of the present invention, adevice for a microarray for personalized diagnostic applicationscomprises: a functional photonic crystal waveguide having a waveguidecore along which light is guided, arrays of photonic crystalmicrocavities along the length of the photonic crystal waveguide eachcoated with a separate biomolecule specific to disease identification,an input and output photonic crystal waveguide with gradually changedgroup index before and after the functional photonic crystal waveguide,which can bridge the refractive indices difference between conventionaloptical waveguides and the functional photonic crystal waveguide. Thesensor can be used to detect organic or inorganic substances such asproteins, DNA, RNA, small molecules, nucleic acids, virus, bacteria,cells, and genes, without requiring labels such as fluorescence orradiometry. Light (from a broadband source or LED) coupled into aphotonic crystal waveguide couples with the resonance of a photoniccrystal microcavity and thereby drops the resonant wavelength in themicrocavity, leading to a minimum in the transmission spectrum of thephotonic crystal waveguide at the resonant wavelength. Transmissionminima are observed for each resonant wavelength of the individualmicrocavities along the photonic crystal waveguide. The resonancewavelength shifts to longer wavelengths in response to the attachment ofa material on the microcavity surface leading to the corresponding shiftof the transmission minimum of that microcavity.

In another embodiment of the present invention, a device for amicroarray for multiple analyte sensing applications comprises: afunctional photonic crystal waveguide having a waveguide core alongwhich light is guided, arrays of photonic crystal microcavities alongthe length of the photonic crystal waveguide each coated with a separatepolymer or hydrogel specific to a unique environmental parameter, aninput and output photonic crystal waveguide with gradually changed groupindex before and after the functional photonic crystal waveguide, whichcan bridge the refractive indices difference between conventionaloptical waveguides and the functional photonic crystal waveguide. Thesensor can be used to detect changes in temperature, pressure, humidity,molarity of solution, acidity or alkalinity (pH) of aqueous medium, ionconcentration of solutions, trace gases in the atmosphere, pollutants inground water that can be organic or inorganic, volatile andnon-volatile, pesticides and thereof in a single optical transmissionmeasurement. A unique polymer or hydrogel is chosen with maximumresponse to changes in each of the above parameters and a uniquemicrocavity along the waveguide is coated with a unique polymer orhydrogel. Light (from a broadband source or LED) coupled into a photoniccrystal waveguide couples with the resonance of a photonic crystalmicrocavity and thereby drops the resonant wavelength in themicrocavity, leading to a minimum in the transmission spectrum of thephotonic crystal waveguide at the resonant wavelength. Transmissionminima are observed for each resonant wavelength of the individualmicrocavities along the photonic crystal waveguide, in the pristinecondition. The resonance wavelength shifts to longer wavelengths inresponse to changes in ambient parameters listed above leading to thecorresponding shift of the transmission minimum of that microcavity, theamount of transmission minimum shift determines the absolute change inambient conditions in the vicinity of the microarray device.

For the measurement of environmental parameters in situ, the device isincorporated with a filter to remove macroscopic dirt and dustparticles. The filter can be a macroscopic filter incorporated off-chipor a microfluidic filter incorporated on-chip.

Methods for fabricating photonic crystal structures are widely describedin the literature. Sensor structures of the invention have highersensitivity than previous structures due to the use of two-dimensionalphotonic crystal microcavities with resonances that have high qualityfactor together with the slow light effect of two-dimensional photoniccrystal waveguides. Methods for patterning of multiple biomoleculesexclusively on photonic crystal microcavities that preserves biomoleculefunctionality in aqueous phase are disclosed. The amount of refractiveindex change and hence the shift in resonance frequency is determined bythe amount of adsorbed molecules or biomolecules on the microcavitysurface that interacts with the electromagnetic field of the photoniccrystal. The system is capable of detecting a single cell attached toits surface.

Microarrays provide an unprecedented opportunity for comprehensiveconcurrent analysis of thousands of biomolecules such as proteins,genes, DNA molecules, small molecules or nucleic acids. The globalanalysis of the response to a toxic agent, as opposed to the historicalmethod of examining a few select biomolecules, provides a more completepicture of toxicologically significant events. Array-based expressionprofiling is useful for differentiating compounds that interact directlywith the species from those compounds that are toxic via a secondarymechanism. Microarrays are consequently finding numerous applications inpathogen detection and biodefense. The sensors have utility in thefields of pharmaceutical research (e.g., high throughput screening,secondary screening, quality control, cytotoxicity, clinical trialevaluation), life science research (e.g., proteomics, proteininteraction analysis, DNA-protein interaction analysis, enzyme-substrateinteraction analysis, cell-protein interaction analysis), diagnostictests (e.g., protein presence, cell identification), environmentaldetection (bacterial and spore detection and identification), andbio-warfare defense.

The principles of the invention can also be applied to e.g., evanescentwave based biosensors and any biosensors incorporating an opticalwaveguide. The principle can also be applied to arrays of ring or diskresonators coupled to a bus waveguide. However such waveguides providelimited free-spectral range for microcavity resonances and also do notincorporate slow light effect of photonic crystal waveguides and arethus less sensitive with low signal-to-noise ratio.

Detailed descriptions of the preferred embodiments are provided herein.It is to be understood, however, that the present invention may beembodied in various forms. Therefore, specific details disclosed hereinare not to be interpreted as limiting, but rather as a basis for theclaims and as representative basis for teaching one skilled in the artto employ the present invention in virtually any appropriately detailedsystem, structure or manner.

Defect engineered photonic crystals, with sub-micron dimensions havealready demonstrated high sensitivity to trace volumes of analytes.While biosensing has been demonstrated in photonic crystal devices withsingle biomolecules, no previous effort has been made to extend thedevice capability to microarrays. Particularly, patterning of multiplebiomolecules on a few micron scales has faced challenges of bindingexclusivity and binding specificity. Our proposed device consists of anarray of photonic crystal microcavity resonators coupled to a singlephotonic crystal waveguide that give rise to minima in the photoniccrystal waveguide transmission spectrum at the resonance frequency ofthe microcavity. Using a new microfluidic technique, individual targetbiomolecules are coated exclusively on individual photonic crystalmicrocavities. Our method eliminates labeling for analyteidentification. The impact of our novel and robust multi-analyte sensingtechnique can reach much further than the field of biomolecular scienceand diagnostics alone. This section will provide detailed description ofthe preferred embodiments in the aspect of device architecture, as wellas the design concept and working principle.

FIG. 1A presents a top view of one embodiment of a photonic crystalmicroarray. It consists of a functional photonic crystal waveguide 100,input ridge waveguide 112, output ridge waveguide 113 and an array of Nphotonic crystal microcavities 20 n where n represents digits and rangesfrom 1 to N (N→∞). The functional photonic crystal waveguide 100includes a number of column members 102 (labeled in FIG. 1B) etchedthrough or partially into the semiconductor slab 101 (labeled in FIG.1B). The waveguide core 141 is defined as the space between the centersof two column members adjacent to the region where the columns areabsent. In one preferred embodiment, the column members 102 (labeled inFIG. 1B) are arranged to form a periodic lattice with a lattice constantα. In some embodiments, the width of waveguide core 141 can range from0.5 times sqrt(3) times the lattice constant α to 50 times sqrt(3) timesthe lattice constant α. The arrows indicate the direction in whichelectromagnetic waves are coupled into and out of the photonic crystalwaveguide respectively. In the figure, due to space limitations, themicrocavities are designated as 201, 202, . . . , 20(n−1) and 20 nrespectively. The photonic crystal microcavities are parallel to thephotonic crystal waveguide and are placed 3 lattice periods away fromthe waveguide. Although the photonic crystal microcavities have beenshown at 3 lattice periods away from the photonic crystal waveguide, theoffset can be 1, 2, . . . 10 lattice periods. Beyond 10 lattice periods,the coupling efficiency of light from the guided light in the photoniccrystal waveguide will be very small. FIG. 1B is an enlarged section ofFIG. 1A showing the photonic crystal microcavity elements 201, 202,columnar members 102, and photonic crystal waveguide 100 in greaterdetail. The photonic crystal waveguide 100 is defined by filling acomplete row of columnar members with the semiconductor slab material101. Similarly, a photonic crystal microcavity, for instance 201, isdefined by filing a row of 4 columnar members 102 with semiconductormaterial 101. The distance between individual photonic crystalmicrocavities is 12 periods. The photonic crystal microcavity 201 canhave different geometries as described in the literature. The resonantwavelength of a photonic crystal microcavity is dependent on thegeometry of the microcavity. Light propagating in a photonic crystalwaveguide couples to a photonic crystal microcavity at the resonantwavelength of the microcavity. The transmission spectrum of the photoniccrystal waveguides consequently shows minima corresponding to theresonant wavelength of each photonic crystal microcavity. With referenceto FIG. 2, which is a cross-sectional view of the functional photoniccrystal waveguide 100 in FIG. 1B taken along line A-A′, the columnmembers 102 extend throughout the thickness of the slab 101 to reach abottom cladding 105. In one embodiment, the top cladding 106 is air.However, the top cladding can be any organic or inorganic dielectricmaterial, columnar members 102 can extend through both 106 and 101 aswell as through the bottom cladding 105 to reach the substrate 107.Although the structure within the slab 101 is substantially uniform inthe vertical direction in this embodiment, vertically non-uniformstructure, such as the columnar members 102 whose radii are varyingalong the vertical direction, may be used as well. The column members102 can be either simply void or filled with other dielectric materials.Between the ridge waveguide 112 and the core photonic crystal waveguide100, there is an impedance taper 115 for coupling of light from ridgewaveguide to photonic crystal waveguide with high efficiency. Similarly,at the output, between the photonic crystal waveguide 100 and the outputridge waveguide 113, there is another impedance taper 114 for bettercoupling efficiency. The impedance taper 115 is formed by shifting thecolumnar members from photonic crystal waveguide 100 to ridge waveguide112 by x times α in the direction perpendicular to 100, in the plane ofthe waveguide, in steps of (x times α)/p where p is a number greaterthan 5, α is the lattice constant, and x varies from 0 to z, where z isa fractional number between zero and one (0<z<1). In FIG. 1A, p equals 8since it is the first eight columnar members that have been shifted inboth of the impedance tapers 115 and 114. In some embodiments, theimpedance tapers 115 and 114 may be oppositely tapered. In thatembodiment, impedance taper 115 would be narrower at the ridge waveguide112 than at the photonic crystal waveguide 100 and impedance taper 114would be narrower at the ridge waveguide 113 than at the photoniccrystal waveguide 100. In this embodiment, x varies from 0 to z, where zis a fractional number between zero and minus one (−1<z<0). For aphotonic crystal waveguide 100, 114 and 115, which comprise photoniccrystals of two-dimensional periodicity, the wave guiding in thevertical direction must be provided by conventional index-guidingscheme. This means a bottom cladding 105 and a superstrate 106 with alower effective index relative to that of the slab material must bedisposed below and above the slab 101. In FIG. 2, the superstrate isabsent and simply represented by air or vacuum. On one side, the bottomcladding 105 and superstrate 106 prevent guided lightwave escaping faraway from the top and bottom surfaces of the slab 101. In mostapplications, it is desirable that the waveguide have a single guidedmode, which can be achieved through adjusting the width of the waveguidecore 141.

In FIG. 3, substances coated on the photonic crystal microcavity arelabeled as 301, 302, . . . 30(n−1), 30 n, where n represents digits andranges from 1 to N (N→∞). Each photonic crystal microcavity 20 n iscoated with a specific substance 30 n. In one embodiment, the substancecan be a biomolecule such as proteins, nucleic acids, DNA, RNA,antigens, antibodies, small molecules, peptides, genes etc. Eachbiomolecule can be specific to a particular disease causing conjugatewhere the disease of interest can be cancer, malaria, Leptospirosis orany infectious disease to achieve specific detection. In anotherembodiment, the substance 30 n can be a hydrogel that swells in thepresence of a specific analytical solution or ambient gas wherein theambient gas includes, but is not limited to, greenhouse gases such ascarbon dioxide, methane, nitrous oxide or other gases such as oxygen,nitrogen thereof. In yet another embodiment, the substance can be apolymer that changes its effective refractive index upon contact with achemical substance or proportionately to changes in temperature,humidity and pressure thereof. The device is therefore a verygeneralized construction where multiple polymer or biological molecules,each specific to detection of a specific species, are arrayed forsimultaneous detection.

FIG. 4 depicts a top view of the field intensity pattern of a guidedmode of a waveguide 100 in FIG. 1 and FIG. 3. The circles indicatecolumnar members of the photonic crystal waveguide. It is seen in FIG. 4that peak of the field intensity is well confined inside the waveguidecore region 141. Outside of 141, there are two side peaks due toevanescent field. Due to even symmetry of the mode with respect to thecenter of the waveguide, the mode couples very well with resonant modesof photonic crystal microcavities which possess even symmetry.

FIG. 5 depicts a top view of the field intensity pattern of a defectmode of a photonic crystal microcavity 20 n where n represents digitsand ranges from 1 to N (N→∞), in FIG. 1 and FIG. 2. The circles indicatecolumnar members of the photonic crystal microcavity. It is seen in FIG.5 that peak of the field intensity is well confined inside the photoniccrystal microcavity region 151. Outside of 151, there is very weak fieldintensity that overlaps with the columnar members. FIG. 5 suggests thatphotonic crystal microcavity resonant mode is well confined in thedielectric, in the plane of the waveguide inside region 151.

The bold curve 190 in FIG. 6 depicts a dispersion diagram of thephotonic crystal waveguide 100. Three regions are distinctly visible inthe bold curve. A region 161 where dω/dk is almost zero, a region 163where dω/dk is very high and a region 162 where dω/dk has intermediatevalues. dω/dk denotes the group velocity of light propagating in thephotonic crystal waveguide at the corresponding frequency. The region164 denotes the stopgap of the photonic crystal waveguide where thetransmission is zero. The coupling efficiency between a photonic crystalwaveguide and a photonic crystal microcavity is inversely proportionalto the group velocity, consequently slower the group velocities higherthe coupling due to higher interaction time. However, region 161 is notsuitable due to high dispersion and consequently high transmission loss.We identify a range of frequencies in region 162 between dotted lines191 and 192 over which we vary the resonance of the photonic crystalmicrocavity to achieve high coupling efficiency with photonic crystalwaveguide 100.

FIG. 7, FIG. 8, FIG. 9 address photonic crystal microcavity designissues so that the entire range of frequencies between the dotted lines191 and 192 can be efficiently used for resonant coupling, therebyincreasing the number of microcavities that can be arrayed in parallelfor the multiple analyte sensing diagnostic chip. FIG. 7A depicts oneembodiment of a photonic crystal microcavity where a row of 4 columnarmembers 102 has been filled with the semiconductor dielectric material101. We consider a photonic crystal waveguide transmission spectrum when2 photonic crystal microcavities say 201 and 202 in FIG. 1 are coupledto the photonic crystal waveguide 100. For the microcavity 201, thecolumnar members 501 and 502, have each been shifted toward each otherby 0.2α and for microcavity 202 the columnar members 503 and 504 haveeach been shifted away from each other by 0.2α, where α denotes thelattice periodicity of the triangular lattice photonic crystalstructure. In FIG. 7B, 2 sharp minima 511 and 512 are observed thatcorrespond to the resonance of corresponding photonic crystalmicrocavities 201 and 202. This demonstrates that progressive geometrytuning of photonic crystal microcavities can result in multiplemicrocavities arrayed along a photonic crystal waveguide, each with aunique resonance frequency resulting in a unique transmission minimum inthe photonic crystal waveguide 100 transmission spectrum. Although themagnitude of the shift is indicated as 0.2α, the magnitude of the shiftcan vary continuously from 0 to 0.45α.

FIG. 8A depicts another embodiment of a photonic crystal microcavitywhere a row of 4 columnar members 102 has been filled with thesemiconductor dielectric material 101. We consider a photonic crystalwaveguide transmission spectrum when 2 photonic crystal microcavitiessay 201 and 202 in FIG. 7A are coupled to the photonic crystal waveguide100. The individual construction of each of the photonic crystalmicrocavities 201 and 202 in FIG. 7A can be described by the microcavityin FIG. 8A. As in FIG. 7A, for the microcavity 201, the columnar members501 and 502, have each been shifted toward each other by 0.2α and formicrocavity 202 the columnar members 503 and 504 have each been shiftedaway from each other by 0.2α, where α denotes the lattice periodicity ofthe triangular lattice photonic crystal structure. For the microcavity202, as illustrated in general for a microcavity 20 n, the diameters ofthe members 601-610 are further reduced in size to 0.9 times thediameter of columnar members 102 elsewhere. Two sharp minima 513 and 514are observed that correspond respectively to the resonance ofcorresponding photonic crystal microcavities 201 and 202. Thetransmission minimum 514 is red-shifted corresponding to thetransmission minimum 512 in FIG. 7B. The transmission minimum 513 is notshifted corresponding to the transmission minimum 511 in FIG. 7B sincethe geometry of microcavity 201 has not been changed from FIG. 7A. Thefact is significant since this ensures that our design selection of 12lattice periods between adjacent microcavities is optimum and does notalter either a resonance quality factor or the resonance wavelength of adesigned microcavity. By reducing the diameter of the columnar members601-610, the dielectric fraction inside the resonant mode of 202 isincreased which brings the frequency of the mode down, closer to thedotted line 192 in FIG. 6. The diameter of the columnar members 601-610can thus be changed in step to achieve a new microcavity design with adifferent resonant frequency. Although the magnitude of the shift forelements 501 and 502 is indicated as 0.2α, the magnitude of the shiftcan vary continuously from 0 to 0.45α. Although the magnitude of thediameter change of the members 601-610 is indicated as 0.9 times thediameter of columnar members 102 elsewhere, the magnitude of the shiftcan vary continuously from 0 to 1 times the diameter of columnar members102 elsewhere.

Referring to FIG. 8A, columnar members 501 and 502 are not the onlycolumnar members that may be shifted. Surrounding columnar members suchas 601-610 may also be shifted towards the interior or exterior of themicrocavity 20 n. In one embodiment, columnar member 501 may be shiftedby 0.2α in the Γ-K direction arrow shown in FIG. 8A, columnar member 502may be shifted by 0.2α in the direction opposite to the Γ-K directionarrow shown in FIG. 8A, all columnar members 601-610 may be shifted by0.2α, in the direction arrows for each element 601-610 shown in FIG. 8A.In another embodiment, columnar member 501 may be shifted by 0.2αopposite to the Γ-K direction arrow shown in FIG. 8A, columnar member502 may be shifted by 0.2α in the direction of the Γ-K direction arrowshown in FIG. 8A, all columnar members 601-610 may be shifted by 0.2α,in the direction opposite to the arrows for each element 601-610 shownin FIG. 8A. Although the magnitude of the shift is indicated as 0.2α,the magnitude of the shift can vary continuously from 0 to 0.45α.Additionally, the columnar members 601-610 may also be shifted at anyangle from 0 to 360 degrees relative to the Γ-K direction arrow in FIG.8A. Similarly, columnar members 501 and 502 may be shifted by 0.2α, atany angle from 0 to 360 degrees relative to the Γ-K direction arrow inFIG. 8A.

FIG. 9 depicts another embodiment of a photonic crystal microcavitywhere a row of 4 columnar members 102 has been filled with thesemiconductor dielectric material 101. We consider a photonic crystalwaveguide transmission spectrum when 2 photonic crystal microcavitiessay 201 and 202 in FIG. 7A are coupled to the photonic crystal waveguide100. For the microcavity 201, the columnar members 501 and 502, havebeen shifted by −0.2α and for microcavity 202 the columnar members 503and 504 are shifted by +0.2α, where α denotes the lattice periodicity ofthe triangular lattice photonic crystal structure. For the microcavity202, the diameters of the members 601-610 are reduced in size to 0.9times the diameter of columnar members 102 elsewhere. For themicrocavity 201, the diameters of the members 601-610 are increased insize to 1.05 times the diameter of columnar members 102 elsewhere. Twosharp minima 515 and 516 are observed that correspond respectively tothe resonance of corresponding photonic crystal microcavities 201 and202. The transmission minimum 515 is blue-shifted corresponding to thetransmission minimum 511 in FIG. 7B. The transmission minimum 516 isred-shifted corresponding to the transmission minimum 514 in FIG. 8B andred-shifted further corresponding to the transmission minimum 512 inFIG. 7B. By further reducing the diameter of the columnar members601-610 compared to FIG. 8B, the dielectric fraction inside the resonantmode of 202 is further increased which brings the frequency of the modedown further, and even closer to the dotted line 192 in FIG. 6. Byincreasing the diameter of the columnar members 601-610, the dielectricfraction inside the resonant mode of 201 is decreased, which raises thefrequency of the resonant mode, closer to the dotted line 191 in FIG. 6.The diameter of the columnar members 601-610 can thus be changed insteps to achieve a new microcavity design with a different resonantfrequency. Although the magnitude of the diameter change of the members601-610 is indicated as 1.05 times the diameter of columnar members 102elsewhere, the magnitude of the shift can vary continuously from 1 to 2times the diameter of columnar members 102 elsewhere. In yet anotherembodiment, the columnar members 501, 502 and 601-610 in FIG. 8A can beselectively filled with a material with the same or different dielectricconstant as the dielectric constant of the slab material to achieve adifferent resonance frequency of the photonic crystal microcavity.

In another embodiment shown in FIG. 8C, the columnar members 501, 501 a,and 501 b and 502, 502 a, and 502 b of microcavity 20 n may be changedin diameter and/or shifted in position to achieve a desired resonancefrequency of the photonic crystal microcavity. By making these and othersimilar geometry changes to the columnar members surrounding themicrocavity as shown for FIG. 7A and FIG. 8A and described for FIG. 9above, for each of the microcavities 201, 202, . . . 20 n in FIG. 1, itis possible to shift the transmission minima of the individualmicrocavities so that they do not overlap. The idea is to have as manyfirst order transmission minima from the varied microcavities withoutinterference from the second order transmission minima. One such secondorder transmission minima from the same microcavity as transmissionminimum 512 can be seen in FIG. 7B just to the left of transmissionminimum 511 at around 1580 nm.

In another embodiment shown in FIG. 8D, each microcavity 201, 202, . . .20 n in FIG. 1A and FIG. 1B may be mirrored or duplicated on theopposite side of the photonic crystal waveguide. The microcavity 201 andthe mirror microcavity 201 a would have the same spacing between voidcolumnar members adjacent to the microcavity 201 and microcavity 201 aand the same diameter of void columnar members adjacent to themicrocavity 201 and microcavity 201 a. The composite microcavity,comprising microcavities 201 and 201 a thus has a larger optical modevolume resulting in higher sensitivity to refractive index changes. Inother embodiments, microcavities oriented along the crystal lattice of+60 degrees and −60 degrees as shown in FIG. 8E and FIG. 8F,respectively, may also be mirrored or duplicated directly across thephotonic crystal waveguide.

In another embodiment shown in FIG. 8E and FIG. 8F, the microcavitiesare oriented along another orientation of the crystal lattice. Althoughthe photonic crystal microcavities 201, 202, . . . 20 n in FIG. 1 havebeen shown parallel to the photonic crystal waveguide, parallel to thedirection of propagation of light in the core, the array can be orientednext to the photonic crystal waveguide along any of the latticedirections at +60 degrees or −60 degrees to the photonic crystalwaveguide as shown in FIG. 8E and FIG. 8F, respectively. Alldescriptions as shown for FIG. 7A and FIG. 8A and described for FIG. 9would be applied similarly with respect to the orientations shown byFIG. 8E and FIG. 8F. Although the photonic crystal microcavities in FIG.8E and FIG. 8F have been shown drawn at 3 periods away from the photoniccrystal waveguide along the respective orientations, the offset can be1, 2, . . . 10 lattice periods. Beyond 10 lattice periods, the couplingefficiency of light from the guided light in the photonic crystalwaveguide will be very small.

The second design concept of this invention is depicted in FIG. 10 thatconcerns the patterning of biomolecules onto the patterned siliconsubstrate 411 using a novel microfluidic technique that preservesbiomolecule functionality in aqueous phase at all times. In oneembodiment, biomolecules are patterned on a photonic crystal patternedsilicon substrate with a thin layer of silicon dioxide. The thickness ofsilicon dioxide is not more than 10 nanometers. FIG. 10 shows the stepsin the fabrication process on a patterned substrate that preserves thebiomolecule functionality in aqueous phase. A film, 412 is deposited onthe substrate in FIG. 10A. In one embodiment, the film 412 is parylene.A thin film of metal 413 is sputtered onto the film 412 and patterned byphotolithography. (FIG. 10B). In one embodiment, the film is aluminumbut it could be any metal that can be sputtered onto the film 412. Using413 mask, 412 is etched to substrate in oxygen plasma. (FIG. 10C). Thefilm 412 is patterned so that only the region above the microcavity isopened. In one embodiment, when the device is to be used as a biosensor,the devices are functionalized by treating with 10% by volume3-aminopropyl-triethoxy-silane (3-APTES) in toluene. It is then washed 3times in toluene to remove unbound 3-APTES, 3 times in methanol toremove toluene and finally 3 times in de-ionized water to removemethanol. The devices are then incubated in 1% glutaraldehyde inphosphate buffered saline (PBS) for 5 minutes and washed 3 times in PBS.Simultaneously, PDMS microfluidic channels are prepared by moldingtechnique. A master silicon wafer 421, cleaned in Piranha solution andrinsed is dried and subsequently, a photoresist 422 is spin-coated onthe silicon wafer. In one embodiment, the photoresist is SU-8 but it canbe any lithographically patterned polymer that can give high aspectratio features. After patterning 422 (FIG. 10D) and baking, a mixture ofanother polymer precursor 423 and curing agent in the ratio of 10:1volume together with a hydrophilic additive is poured over the 422 mold,as shown in FIG. 10E. In this embodiment the polymer 423 ispolydimethylsiloxane, popularly known as PDMS. After complete curing,the 423 layer will be removed from the mold to achieve the structure asshown in FIG. 10F. The PDMS microfluidic channel is carefully alignedand mounted on the structure patterned in FIG. 10C, as shown in FIG.10G. Solutions 433 containing different biomolecule samples 431, 432will be introduced into microchannels as illustrated in FIG. 10H.Biomolecules will be selectively deposited on exposed sites in eachchannel on the photonic crystal microcavity. After initial biomoleculedeposition and overnight incubation, microchannels will be thoroughlywashed with PBS to purge them of any excess, unbound biomolecule and themicrochannels peeled off using tweezers. After overnight incubation andwashing, the device is coated with bovine serum albumin (BSA) to preventany non-specific binding and washed 3 times with PBS. Finally, thedevice as a whole is maintained in solution 433 as shown in FIG. 10I.The final photonic crystal microcavities coupled to waveguide microarraydevice with patterned proteins has been shown schematically in FIG. 3.

In another embodiment, the individual biomolecules are dispensed on topof the individual photonic crystal microcavities by an ink jet printer.In this embodiment, devices are functionalized by treating with 10% byvolume 3-APTES in toluene. It is then washed 3 times in toluene toremove unbound 3-APTES, 3 times in methanol to remove toluene andfinally 3 times in de-ionized water to remove methanol. The devices arethen incubated in 1% glutaraldehyde in phosphate buffered saline (PBS)for 5 minutes and washed 3 times in PBS. Target biomolecules in glycerolare ink-jet printed with precision on top of the photonic crystalmicrocavities. A unique biomolecule 301 is printed on individualphotonic crystal microcavity 201. The printed spots were left toincubate overnight. Subsequently, all target antibodies not bound to thefunctionalized device layer were removed by washing 3 times in PBS.After overnight incubation and washing, the device is coated with bovineserum albumin (BSA) to prevent any non-specific binding and washed 3times with PBS. No microfluidic channels are needed in this embodiment.The final photonic crystal microcavities coupled to waveguide microarraydevice with patterned proteins has been shown schematically in FIG. 3.

FIG. 11 is the top view of the device in FIG. 10G and FIG. 10H. Asillustrated, openings in the parylene (412) are lithographically definedso that the photonic crystal microcavity regions of 201 and 202 areexposed. The procedure applies to all microcavities 20 n. The PDMSmicrochannels are depicted by the dotted elements 423. Molecules andtarget biomolecules 431 and 432 corresponding respectively tobiomolecular specific coatings on photonic crystal microcavities 201 and202 are flown in through the microfluidic channels in the direction ofthe arrows. Biomolecules 431 and 432 correspond to 301 and 302respectively in FIG. 3. Since the open areas in 412 have been silanized,biomolecules 301 (431) and 302 (432) preferentially bind to the photoniccrystal substrate above the photonic crystal microcavities 201 and 202respectively. The same principle applies to all N photonic crystalmicrocavities arrayed along the length of the photonic crystal waveguide100. Thus, there is no cross-contamination between 301 (431) and 302(432).

FIG. 12A and FIG. 12B show how the detection sensitivity can beamplified as well as how more confidence is derived regarding theselectivity or specificity of the binding between an analyte molecule orbiomolecule and its corresponding molecule or biomolecule on the one ormore optical microcavities. The detection sensitivity of the device isdetermined from the magnitude of the shift in the minimum in thetransmission intensity corresponding to the magnitude of the change inthe resonance frequency of the resonance mode of the correspondingphotonic crystal microcavity. The specificity of the detection isdetermined by the binding of the analyte molecule or biomolecule only tospecific polymer molecules or biomolecules. Sensitivity amplification isachieved by an enhancement of the magnitude of the shift by thesecondary molecule or biomolecule. Enhancement of detection specificityis achieved by the binding of the analyte molecule or biomolecule to twopolymer molecules or biomolecules, namely, the polymer molecule orbiomolecule attached to the photonic crystal microcavity device, and thesecondary polymer molecule or biomolecule introduced in solution. Theprinciple is described with respect to the resonance 515 in FIG. 9. Weconsider that λ₅₁₅₁ is the minimum in the transmission wavelengthcorresponding to the resonance 5151 of the particular photonic crystalmicrocavity 201 that is coated with a polymer molecule or biomolecule301 as in FIG. 3. We consider that λ₅₁₆₁ is the minimum in thetransmission wavelength corresponding to the resonance 5161 of theparticular photonic crystal microcavity 202 that is coated with apolymer molecule or biomolecule 302 as in FIG. 3. When an analytemolecule or biomolecule 3011 that binds to 301 is introduced insolution, a resonance wavelength shift is observed and the resonanceminimum λ₅₁₅₁ in the transmission spectrum shifts to the new wavelengthposition λ₅₁₅₂ corresponding to the changed resonance 5152 of thephotonic crystal microcavity 201 coated with polymer molecule orbiomolecule 301. The net wavelength shift is thus (λ₅₁₅₂ minus λ₅₁₅₁)where λ₅₁₅₂ is greater in magnitude than λ₅₁₅₁. No resonance wavelengthshift will be observed in the resonance λ₅₁₆₁. When a secondary polymermolecule or biomolecule 3012 is next introduced in solution, which alsobinds to the analyte molecule or biomolecule 3011 that has bound to 301,a secondary resonance wavelength shift is observed and the transmissionminimum λ₅₁₅₂ shifts to a new transmission minimum λ₅₁₅₃ correspondingto the further modified resonance frequency of the photonic crystalmicrocavity 201. The analyte molecule or biomolecule 3011 is thussandwiched between the two polymer molecules or biomolecules 301 and3012, both of which recognize the analyte molecule or biomolecule 3011.No resonance wavelength shift is observed in the transmission minimum atλ₅₁₆₁ corresponding to the resonance 5161 that corresponds to theresonance frequency of the photonic crystal microcavity 202 that iscoated with a polymer molecule or biomolecule 302 that does not bind tothe analyte molecule or biomolecule 3012. The secondary wavelength shiftdue to the sandwich thus amplifies the resonance wavelength shift of thecorresponding photonic crystal microcavity to (λ₅₁₅₃ minus λ₅₁₅₁) where(λ₅₁₅₃ minus λ₅₁₅₁) is greater than (λ₅₁₅₂ minus λ₅₁₅₁) and represents amethod of amplifying the sensitivity in label-free optical microarrays.In addition, the secondary wavelength shift due to the sandwich furtherproves that the analyte molecule or biomolecule 3011 that has bound to301 on top of the photonic crystal microcavity 201 is indeed the analytemolecule or biomolecule 3011 that must be detected and is not any othernon-selective molecule or biomolecule which sticks to the molecule orbiomolecule due to other physical reasons not determined by the bindingkinetics between 301 and 3011. In addition to sensitivity amplification,the sandwiched detection method applied to the photonic crystal labelfree microcavity thus adds to detection specificity and detectionselectivity. The sensor surface 201 may be regenerated by removing theanalyte molecules or biomolecules 3011 and the secondary molecules orbiomolecules 3012 by subjecting the sensor device to appropriatesolutions such as solutions with a low pH. Consequently, in FIG. 12A andFIG. 12B, after regeneration, the resonance wavelength λ₅₁₅₃ or λ₅₁₅₂returns to λ₅₁₅₁.

Although the method in FIG. 12A and FIG. 12B above has been describedwith respect to photonic crystal microcavities 201 and 202, one skilledin the art will note that the method can be applied with respect to allphotonic crystal microcavities 201, 202, . . . 20(n−1), 20 n in FIG. 1A.

In one embodiment, the slab 101 is formed from a material of highrefractive index including, but not limited to, silicon, germanium,carbon, gallium nitride, gallium arsenide, gallium phosphide, indiumnitride, indium phosphide, indium arsenide, zinc oxide, zinc sulfide,silicon oxide, silicon nitride, alloys thereof, metals, and organicpolymer composites. Single crystalline, polycrystalline, amorphous, andother forms of silicon may be used as appropriate. Organic materialswith embedded inorganic particles, particularly metal particles, may beused to advantage. In one embodiment, the top cladding 106 and bottomcladding 105 are formed from a material whose refractive index is lowerthan that of the slab material. Suitable top cladding and bottomcladding materials include, but not limited to, air, silicon oxide,silicon nitride, alumina, organic polymers and alloys thereof. Thesubstrate 107 materials include, but not limited to, silicon, galliumarsenide, indium phosphide, gallium nitride, sapphire, glass, polymerand alloys thereof. In one embodiment, the columnar members 102 areformed from a material whose refractive index is substantially differentfrom that of the slab 101. Suitable materials for the columnar members102 include, but not limited to, air, silicon oxide, silicon nitride,alumina, organic polymers, or alloys thereof. In one preferredembodiment, the slab 101 is formed from silicon, the columnar members102 are formed from air, the top cladding 106 is air, and the bottomcladding 105 is formed from silicon oxide, while the substrate 107 issilicon.

Although the word “biomolecule” is used in the preceding discussions,one skilled in the art will understand that it refers to a general formof biomolecule that includes, but not limited to, proteins,deoxyribonucleic acid (DNA), ribonucleic acid (RNA), genes, antigens,antibodies, small molecules, nucleic acids, bacteria, viruses and anyarrayed combination thereof for the specific diagnosis of diseases.“Molecule” can denote any polymer or hydrogel that responds to changesin the ambient medium of the device. Any combination of “molecules” and“biomolecules” can be arrayed on the device to get precise knowledge ofprocess conditions, system conditions, analyte identification and/orbinding events for disease identification.

Although the word “light” or “lightwave” is used to denote signals inthe preceding discussions, one skilled in the art will understand thatit refers to a general form of electromagnetic radiation that includes,and is not limited to, visible light, infrared light, ultra-violetlight, radios waves, and microwaves.

In summary, the present invention provides an ultra compact microarraydevice architecture using two-dimensional photonic crystal microcavitiescoupled to a single photonic crystal waveguide, together with a newmicrofluidic technique that preserves the biomolecule functionality inaqueous phase. The invention enables massively parallel, label-free,on-chip multi-analyte sensing for biochemical sensing and a diagnosticassay for any disease, which displays target-probe biomoleculeconjugation. The biomolecule of interest can be DNA, RNA, proteins,nucleic acids and small molecules. It incorporates a new microfluidictechnique with photonic crystal devices, that allows patterning ofbiomolecules in the aqueous phase. Owing to the small dimensions of thedevices presented herein, one can monolithically integrate the photoniccrystal microarrays on silicon VLSI chips. The CMOS compatible photoniccrystal microarray devices have simpler design requirements than themicroelectronics industry. Furthermore, easy regeneration capability andhigh measurement throughput ensures that our miniature compact deviceswill deliver improved results with significantly lower cost to thecustomer. The device is of extreme significance in basic biologicalsciences and human health diagnostics, as well as in the food andbeverage industry and in bio-warfare defense.

While the invention has been described in connection with a number ofpreferred embodiments, it is not intended to limit the scope of theinvention to the particular form set forth, but on the contrary, it isintended to cover such alternatives, modifications, and equivalents asmay be included within the design concept of the invention as defined bythe appended claims.

The invention claimed is:
 1. A method for preparing a device fordetecting one or more label-free analytes and detecting the one or morelabel-free analytes, the method comprising: generating electromagneticradiation from a broadband source; coupling the electromagneticradiation generated by the broadband source to the device for detectingone or more label-free analytes, wherein the device comprises: i) asubstrate; ii) a slab disposed on the substrate; iii) a plurality ofvoid columnar members etched through the slab, wherein the plurality ofvoid columnar members form a periodic lattice with a lattice constant α;iv) a core in the slab having an input side and an output side; v) aphotonic crystal waveguide formed within the core by a row of voidcolumnar members from the input side to the output side, wherein the rowof void columnar members is filled with the material of the slab; vi) aninput impedance taper in the photonic crystal waveguide at the inputside; vii) an input ridge waveguide in the core coupled to the inputimpedance taper in the photonic crystal waveguide, along the slab,wherein the input impedance taper is configured to couple theelectromagnetic radiation between the input ridge waveguide and thecore; viii) an output impedance taper in the photonic crystal waveguideat the output side; ix) an output ridge waveguide in the core coupled tothe output impedance taper in the photonic crystal waveguide, along theslab, wherein the output impedance taper is configured to couple theelectromagnetic radiation between the core and the output ridgewaveguide; and x) an array of photonic crystal microcavities, whereinthe array of photonic crystal microcavities comprise one or more opticalmicrocavities formed by a group of columnar members, wherein the groupof columnar members is filled with the material of the slab and whereinthe one or more optical microcavities are at an angle of +60 degrees or−60 degrees relative to the core and are separated from each other andthe photonic crystal waveguide by one or more lattice constants; xi)wherein the photonic crystal waveguide supports one or more guided modesof the electromagnetic radiation generated by the broadband source; xii)wherein each of the one or more optical microcavities are uniquely tunedto support one or more resonance modes; xiii) wherein the one or moreoptical microcavities are tuned by changing at least one of: the spacingof the void columnar members adjacent to the one or more opticalmicrocavities and the diameter of the void columnar members adjacent tothe one or more optical microcavities; xiv) wherein each of the one ormore optical microcavities along the photonic crystal waveguide has aunique resonance frequency that does not overlap with the resonancefrequency of any other optical microcavity along the photonic crystalwaveguide; xv) wherein the array of photonic crystal microcavities withone or more target binding molecules coated on the array of photoniccrystal microcavities uniquely support one or more resonance modescomprising one or more unique resonant frequencies trapped by the arrayof photonic crystal microcavities resulting in unique minima in atransmission spectrum of the one or more guided modes of the broadbandsource at the corresponding resonant frequencies of the one or moreoptical microcavities; and xvi) wherein the one or more label-freeanalytes selectively bind to the one or more target binding moleculesresulting in shifting the one or more resonant frequencies of thecorresponding one or more optical microcavities and hence the minima inthe transmission spectrum of the one or more guided modes of thebroadband source; coating the one or more target binding molecules ontothe array of photonic crystal microcavities; measuring a firsttransmission spectrum, wherein measuring the first transmission spectrumcomprises measuring the electromagnetic radiation from the output ridgewaveguide of the device; identifying a first minimum of the firsttransmission spectrum; exposing the device to the one or more label-freeanalytes to allow the selective binding of the one or more label-freeanalytes to the one or more target binding molecules coated on the arrayof photonic crystal microcavities; measuring a second transmissionspectrum, wherein measuring the second transmission spectrum comprisesmeasuring the electromagnetic radiation from the output ridge waveguideof the device; identifying a second minimum of the second transmissionspectrum; comparing the second minimum of the second transmissionspectrum with the first minimum of the first transmission spectrum; andidentifying the one or more label-free analytes from the comparisonbetween the second minimum of the second transmission spectrum with thefirst minimum of the first transmission spectrum.
 2. The method of claim1, wherein the device further comprises one or more additional targetbinding molecules selectively bound to the one or more label-freeanalytes to form a sandwich in which the analyte is held between the oneor more target binding molecules and the one or more additional targetbinding molecules resulting in an additional shift in the resonancefrequencies of the one or more optical microcavities and hence theminima in the transmission spectrum of the one or more guided modes ofthe broadband source.
 3. The method of claim 1, wherein the devicefurther comprises one or more optical microcavities mirrored orduplicated directly across the photonic crystal waveguide.
 4. The methodof claim 1, wherein the input impedance taper comprises first p pairs ofvoid columnar members across the core immediately adjacent both sides ofthe core from the input side separated by the width of the core plus 2xtimes α, where x ranges from z to 0 in decrements of (x times α)/p,where p is a number greater than 5 and z is a fractional number between0 and 1; and wherein the output impedance taper comprises first p pairsof void columnar members across the core immediately adjacent both sidesof the core from the output side separated by the width of the core plus2x times α, where x ranges from z to 0 in decrements of (x times α)/p,where p is a number greater than 5 and z is a fractional number between0 and
 1. 5. The method of claim 1, wherein the input impedance tapercomprises first p pairs of void columnar members across the coreimmediately adjacent both sides of the core from the input sideseparated by the width of the core plus 2x times α, where x ranges fromz to 0 in decrements of (x times α)/p, where p is a number greater than5 and z is a fractional number between −1 and 0; and wherein the outputimpedance taper comprises first p pairs of void columnar members acrossthe core immediately adjacent both sides of the core from the outputside separated by the width of the core plus 2x times α, where x rangesfrom z to 0 in decrements of (x times α)/p, where p is a number greaterthan 5 and z is a fractional number between −1 and
 0. 6. The method ofclaim 1, wherein the device is further configured with tuned frequenciesof the one or more guided modes, wherein the frequencies of the one ormore guided modes are tuned by changing at least one of: the diameter ofthe void columnar members, the spacing of the void columnar members, thewidth of the slab, and the thickness of the slab.
 7. The method of claim1 wherein the width of the photonic crystal waveguide can vary from 0.5times sqrt(3) times α to 50 times sqrt(3) times α.
 8. The method ofclaim 1, wherein the material of the slab is selected from the groupconsisting of: silicon, germanium, carbon, gallium nitride, galliumarsenide, gallium phosphide, indium nitride, indium phosphide, indiumarsenide, zinc oxide, silicon oxide, silicon nitride, alloys thereof,and organic polymers.
 9. The method of claim 1, wherein the devicefurther comprises a plurality of void columnar members filled withmaterial selected from the group consisting of: air, silicon oxide,silicon nitride, and organic polymers, and wherein the material selectedfor filling the plurality of void columnar members is different than thematerial of the slab.
 10. The method of claim 1, wherein the devicefurther comprises each of the one or more optical microcavities of thearray of photonic crystal microcavities coated with different targetbinding molecules.
 11. The method of claim 1, wherein the device furthercomprises one or more microfluidic channels arrayed orthogonal to thephotonic crystal waveguide and parallel to the slab to eliminatecross-contamination between the one or more target binding molecules.12. The method of claim 1, wherein the device further comprises the oneor more target binding molecules preserved in an aqueous phase.
 13. Themethod of claim 1, wherein the one or more target binding moleculescomprise proteins, deoxyribonucleic acid, ribonucleic acid, smallmolecules, genes, nucleic acids, antigens, or antibodies, each of whichshows a specific response to its specific conjugate antigen in blood,serum, saliva or animal fluid.
 14. The method of claim 1, wherein theone or more target binding molecules change refractive index with achange in ambient conditions including but not limited to temperature,pressure, humidity, presence of trace gases (greenhouse andnon-greenhouse), groundwater contaminants (organic/inorganic,volatile/non-volatile), and pesticides.
 15. The method of claim 1,wherein the one or more target binding molecules coated on the array ofphotonic crystal microcavities are regenerated by removing the bound oneor more label-free analytes and the bound one or more additional targetbinding molecules.
 16. The method of claim 1, wherein the device furthercomprises a filter configured to filter out particles from thelabel-free analyte and wherein the filter comprises an on-chipmicrofluidic filter or an off-chip macroscopic filter.